--- a
+++ b/4-Multi-Omic Integration/scripts/3.mediation_metaB.2.hostT.r
@@ -0,0 +1,131 @@
+# files required:
+# 1) MetaB module abundance table ("1_metaB.module_eigengene.txt") generated by WGCNA
+# 2) HostT module abundance table ("1_hostT.module_eigengene.txt") generated by WGCNA
+# 3) meta data ("meta.mediation.NEU.txt") containing clinical variable NEU
+# 4) significant HostT modules ("2_significant_HostT_modules.RData") generated from script '3.significant.hostT.modules.r'
+# 5) significant MetaB modules ("2_significant_MetaB_modules.RData") generated from script '3.significant.metaB.modules.r'
+
+# output:
+# File "MetaB_affects_NEU_through_HostT.txt" recording ACME.p,	ADE.p, and	prop.mediated of each mediation route (MetaB module -- HostT module -- clinical variable NEU)
+
+Treat.omic = "MetaB"
+Mediator.omic = "HostT"
+Y = "NEU"
+
+load("2_significant_MetaB_modules.RData")
+Treat.omic.sigModules <- MetaB.sigMods.NEU
+load("2_significant_HostT_modules.RData")
+Mediator.omic.sigModules <- HostT.sigMods.NEU
+outputDir = "Output"
+log.file = "mediation.MetaB2HostT.log"
+
+library(mediation)
+MetaB.Mod.dat <- fread("1_metaB.module_eigengene.txt",data.table = F) %>%
+  dplyr::filter(!grepl("#",`#NAME`,fixed=T)) 
+MetaB.Mod.dat[-1] <- sapply(MetaB.Mod.dat[-1], as.numeric)
+MetaB.Mod.dat <- MetaB.Mod.dat %>% tibble::column_to_rownames("#NAME")
+m1 = MetaB.Mod.dat
+feature.abb_df1 <- cbind.data.frame(feature = rownames(m1),
+                                    abb = paste("feature",seq(1,nrow(m1),1),sep = ""),
+                                    stringsAsFactors = F)
+rownames(m1) <- sapply(rownames(m1), function(x) feature.abb_df1$abb[which(feature.abb_df1$feature == x)])
+m1 <- t(m1) %>% as.data.frame(stringsAsFactors=F)
+colnames(m1) <- sapply(colnames(m1), function(x) feature.abb_df1$feature[which(feature.abb_df1$abb == x)])
+
+HostT.Mod.dat <- fread("1_hostT.module_eigengene.txt",data.table = F) %>%
+  dplyr::filter(!grepl("#",`#NAME`,fixed=T)) 
+HostT.Mod.dat[-1] <- sapply(HostT.Mod.dat[-1], as.numeric)
+HostT.Mod.dat <- HostT.Mod.dat %>% tibble::column_to_rownames("#NAME")
+m2 <- HostT.Mod.dat
+feature.abb_df2 <- cbind.data.frame(feature = rownames(m2),
+                                    abb = paste("feature",seq(1,nrow(m2),1),sep = ""),
+                                    stringsAsFactors = F)
+rownames(m2) <- sapply(rownames(m2), function(x) feature.abb_df2$abb[which(feature.abb_df2$feature == x)])
+m2 <- t(m2) %>% as.data.frame(stringsAsFactors=F)
+colnames(m2) <- sapply(colnames(m2), function(x) feature.abb_df2$feature[which(feature.abb_df2$abb == x)])
+
+
+feature.abb_df2 <- cbind.data.frame(feature = rownames(m2),
+                                    abb = paste("feature",seq(1,nrow(m2),1),sep = ""),
+                                    stringsAsFactors = F)
+rownames(m2) <- sapply(rownames(m2), function(x) feature.abb_df2$abb[which(feature.abb_df2$feature == x)])
+m2 <- t(m2) %>% as.data.frame(stringsAsFactors=F)
+colnames(m2) <- sapply(colnames(m2), function(x) feature.abb_df2$feature[which(feature.abb_df2$abb == x)])
+
+
+
+meta_df <- fread("meta.mediation.NEU.txt", data.table = F)
+
+if(!dir.exists(outputDir)) dir.create(outputDir)
+
+cat(paste(as.character(Sys.time()), '\n'),  file=log.file, append=T)
+cat('Performing mediation analysis: \n',  file=log.file, append=T)
+
+Mediation.results <- NULL
+for(md1 in Treat.omic.sigModules){
+  
+  for(md2 in Mediator.omic.sigModules){
+    
+    id = paste(Treat.omic, ".", md1, "_", Mediator.omic, ".", md2, "_", Y,sep = "" )
+    cat(paste(id, "\n", sep = ""),  file=log.file, append=T)
+    
+    dat <- base::merge(base::merge(meta_df, m1 %>% dplyr::select(all_of(md1)), by.x = "SampleID", by.y = 0),
+                       m2 %>% dplyr::select(all_of(md2)), by.x = "SampleID", by.y=0)
+    
+    colnames(dat)[(ncol(dat)-1):ncol(dat)] <- c("Treat", "Mediator")
+    
+    # write.table(dat, file = paste(outputDir, "/",Treat.omic, "_", md1, "_", Mediator.omic, "_", md2,".txt",sep = ""),
+    #             quote = F, row.names = F, sep = "\t")
+    
+    colnames(dat)[which(colnames(dat) == Y)] <- "Y"
+    
+    # remove na
+    
+    dat <- dat %>% filter(!is.na(Y)) %>% filter(!is.na(Treat)) %>% filter(!is.na(Mediator))
+    
+    #model.m=lm(Mediator ~ Treat+Age+Gender+CurrentSmoking+ICS,dat)
+    model.m = lm(as.formula( paste("Mediator ~ Treat + ", 
+                                   paste(colnames(dat)[!(colnames(dat) %in% c("SampleID","Y","Mediator","Treat"))], collapse = " + "),
+                                   sep = "") ), data = dat)
+    
+    #model.y=lm(Y~Treat+Mediator+Age+Gender+CurrentSmoking+ICS,dat)
+    model.y = lm(as.formula( paste("Y ~ Treat + Mediator + ", 
+                                   paste(colnames(dat)[!(colnames(dat) %in% c("SampleID","Y","Mediator","Treat"))], collapse = " + "),
+                                   sep = "") ), data = dat)
+    
+    summary = summary(mediate(model.m,model.y,treat="Treat",mediator="Mediator",boot=F,sims=1000))
+    #capture.output(summary,file="mediator_out.txt",append=FALSE)
+    res <- capture.output(summary,append=FALSE)
+    
+    #sub( "^()\\s", "\\1", res[7])
+    tmp <-  base::strsplit(res[grep("ACME",res)],"\\s")[[1]]
+    tmp <- tmp[tmp != "" & tmp!="."]
+    tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
+    ACME.p <- tmp[length(tmp)]
+    
+    tmp <- base::strsplit(res[grep("ADE",res)],"\\s")[[1]]
+    tmp <- tmp[tmp != "" & tmp!="."]
+    tmp <- tmp[!grepl("*",tmp,fixed = T) ]
+    ADE.p <- tmp[length(tmp)]
+    
+    tmp <- base::strsplit(res[grep("Prop. Mediated", res)],"\\s")[[1]]
+    tmp <- tmp[tmp != "" ]
+    i_str = which(grepl("Mediated", tmp))
+    prop.mediated <- tmp[(i_str + 1)]
+    
+    spearman.r = cor(dat$Treat, dat$Mediator, method = "spearman")
+    
+    
+    
+    vec = c(id, ACME.p, ADE.p, prop.mediated, spearman.r)
+    names(vec) <- c("Treat_Mediator_Y", "ACME.p", "ADE.p", "prop.mediated", "spearman.r")
+    
+    Mediation.results <- bind_rows(Mediation.results, vec)
+    
+  }
+}
+
+cat('Mediation analysis generates a result file named Treat_affects_Y_through_Mediator.txt. \n ',  file=log.file, append=T)
+write.table(Mediation.results, file = paste(outputDir, "/3_", Treat.omic,"_affects_", Y, "_through_", Mediator.omic,".txt",sep = "" ),
+            quote = F, row.names = F, sep = "\t")
+